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RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, alinear heteropolymer, using a single stranded DNA (ssDNA) as the correspondingtemplate; the sequence of monomers of the RNA is dictated by that of monomerson the ssDNA template. While polymerizing a RNA, the RNAP walks step-by-step onthe ssDNA template in a specific direction. Thus, a RNAP can be regarded alsoas a molecular motor and the sites of start and stop of its walk on the DNAmark the two ends of the genetic message that it transcribes into RNA.Interference of transcription of two overlapping genes is believed to regulatethe levels of their expression, i.e., the overall rate of the corresponding RNAsynthesis, through suppressive effect of one on the other. Here we model thisprocess as a mixed traffic of two groups of RNAP motors that are characterizedby two distinct pairs of start and stop sites. Each group polymerizes identicalcopies of a RNA while the RNAs polymerized by the two groups are different.These models, which may also be viewed as two interfering totally asymmetricsimple exclusion processes, account for all modes of transcriptionalinterference in spite of their extreme simplicity. A combination of mean-fieldtheory and computer simulation of these models demonstrate the physical originof the switch-like regulation of the two interfering genes in bothco-directional and contra-directional traffic of the two groups of RNAP motors.

Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression